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src/p/y/pynast-1.2.2/pynast/util.py   pynast(Download)
from cogent.app.formatdb import build_blast_db_from_seqs, \
 build_blast_db_from_fasta_path
from cogent.app.muscle_v38 import align_unaligned_seqs as muscle_align_unaligned_seqs
from cogent.app.mafft import align_unaligned_seqs as mafft_align_unaligned_seqs
from cogent.app.clustalw import align_unaligned_seqs as clustal_align_unaligned_seqs

src/c/o/cogent-1.5.3/tests/test_app/test_muscle_v38.py   cogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.muscle_v38 import Muscle, muscle_seqs, aln_tree_seqs, \
        align_unaligned_seqs, build_tree_from_alignment, \
        align_and_build_tree, add_seqs_to_alignment, align_two_alignments
    def test_align_unaligned_seqs(self):
        """align_unaligned_seqs should work as expected"""
        res = align_unaligned_seqs(self.seqs1, RNA)
        self.assertEqual(res.toFasta(), align1)
 

src/p/y/pycogent-HEAD/tests/test_app/test_muscle_v38.py   pycogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.muscle_v38 import Muscle, muscle_seqs, aln_tree_seqs, \
        align_unaligned_seqs, build_tree_from_alignment, \
        align_and_build_tree, add_seqs_to_alignment, align_two_alignments
    def test_align_unaligned_seqs(self):
        """align_unaligned_seqs should work as expected"""
        res = align_unaligned_seqs(self.seqs1, RNA)
        self.assertEqual(res.toFasta(), align1)
 

src/p/y/pynast-1.2.2/tests/test_util.py   pynast(Download)
from cogent.util.misc import remove_files
from cogent.core.alignment import DenseAlignment
from cogent.app.muscle_v38 import align_unaligned_seqs as muscle_align_unaligned_seqs
from cogent.app.mafft import align_unaligned_seqs as mafft_align_unaligned_seqs
from cogent.app.clustalw import align_unaligned_seqs as clustal_align_unaligned_seqs